In [1]:
%load_ext autoreload
%autoreload 2
import os
import sys
import numpy as np
import pandas as pd
# Import custom modelling code
module_path = os.path.abspath(os.path.join('../'))
if module_path not in sys.path:
sys.path.append(module_path)
from src.models.run_model import *
from src.visualization.visualize import *
import src.features as features
In [2]:
flora_data_frame = pd.read_csv("../data/processed/flora_data_frame_full.csv", index_col=0)
flora_data_frame['dataset_name'].value_counts().plot.bar()
plt.show()
flora_data_frame[['classification', 'dataset_name', 'text']] \
.groupby(['classification', 'dataset_name']).count().plot.bar()
Out[2]:
View a word cloud for all text data¶
Text is processed using the same custom (bare-bones) tokenizer and stopwords used to train the model.
In [3]:
tokenized_stop_words = features.prepare_stop_words(custom_stop_words=["unknown", "accepted", "synonym",
"basionym", "source",
"note", "notes", "morphology", "fna_id"]) # Find a way to keep numbers and elipses!
# morphology word is an artefact of the FNA xml key statements.
# TODO Return to this and fix
text = " ".join(text_string for text_string in flora_data_frame.text)
visualize_words(text, tokenized_stop_words)
What does the word cloud look like if we apply a strict preprocessing cleaning regime?¶
In [4]:
tokenized_stop_words_clean = features.prepare_stop_words(custom_stop_words=["unknown", "accepted", "synonym",
"basionym", "source",
"note", "notes", "morphology", "fna_id"], clean=True)
visualize_words(text, tokenized_stop_words_clean, cleanup=True)
Generate word clouds by classification.¶
Are there any noticeable differences between the words used most frequently between the classifications?
In [5]:
taxon_identification = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.classification == "taxon_identification"].text)
morphology = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.classification == "morphology"].text)
key = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.classification == "key"].text)
habitat = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.classification == "habitat"].text)
Taxon identification
In [75]:
visualize_words(taxon_identification, tokenized_stop_words, color="purple")
visualize_words(taxon_identification, tokenized_stop_words_clean, cleanup=True, color="purple")
Morphology
In [7]:
visualize_words(morphology, tokenized_stop_words, color="red")
visualize_words(morphology, tokenized_stop_words_clean, cleanup=True, color="red")
Keys
In [8]:
visualize_words(key, tokenized_stop_words, color="yellow")
visualize_words(key, tokenized_stop_words_clean, cleanup=True, color="yellow")
Habitat
In [74]:
visualize_words(habitat, tokenized_stop_words, color="blue")
visualize_words(habitat, tokenized_stop_words_clean, cleanup=True, color="blue")
Word clouds by flora source¶
Are there differences between training sets in the most commonly used words?
In [10]:
bc_text = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.dataset_name == 'bc'].text if text_string not in tokenized_stop_words)
budds_text = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.dataset_name == 'budds'].text if text_string not in tokenized_stop_words)
fna_text = " ".join(text_string for text_string in flora_data_frame[flora_data_frame.dataset_name == 'fna'].text if text_string not in tokenized_stop_words)
BC
In [11]:
visualize_words(bc_text, tokenized_stop_words)
visualize_words(bc_text, tokenized_stop_words_clean, cleanup=True)
FNA
In [12]:
visualize_words(fna_text, tokenized_stop_words)
visualize_words(fna_text, tokenized_stop_words_clean, cleanup=True)
Budds
In [13]:
visualize_words(budds_text, tokenized_stop_words)
visualize_words(budds_text, tokenized_stop_words_clean, cleanup=True)
Visualize distinctive words using tf-idf¶
In [14]:
custom_vec = TfidfVectorizer(lowercase=True, tokenizer=features.flora_tokenizer, stop_words=tokenized_stop_words, ngram_range=(1, 1))
text_counts = custom_vec.fit_transform(flora_data_frame['text']) # Build TF-IDF Matrix
scores = zip(custom_vec.get_feature_names(), np.asarray(text_counts.sum(axis=0)).ravel())
sorted_scores = sorted(scores, key=lambda x: x[1], reverse=True)
#for item in sorted_scores:
# print("{0:10} Score: {1}".format(item[0], item[1]))
sorted_scores_df = pd.DataFrame(sorted_scores, columns=['word', 'score']).iloc[:50]
sorted_scores_df.plot.bar(x='word', y='score')
plt.show()
Distinctive words with new cleaning regime
In [15]:
custom_vec = TfidfVectorizer(lowercase=True, tokenizer=features.flora_tokenizer_clean, stop_words=tokenized_stop_words_clean, ngram_range=(1, 1))
text_counts = custom_vec.fit_transform(flora_data_frame['text']) # Build TF-IDF Matrix
scores = zip(custom_vec.get_feature_names(), np.asarray(text_counts.sum(axis=0)).ravel())
sorted_scores = sorted(scores, key=lambda x: x[1], reverse=True)
#for item in sorted_scores:
# print("{0:10} Score: {1}".format(item[0], item[1]))
sorted_scores_df = pd.DataFrame(sorted_scores, columns=['word', 'score']).iloc[:50]
sorted_scores_df.plot.bar(x='word', y='score')
plt.show()
Run a DTM based model and a TFIDF based model and review accuracy¶
In [16]:
# ==== DTM =====
custom_vec, dtm_text_counts = build_dtm_text_counts(features.flora_tokenizer, tokenized_stop_words, flora_data_frame)
dtm_y_test, dtm_predictions = run_model(dtm_text_counts, flora_data_frame, feature_rank=True, custom_vec)
# ==== TFIDF =====
custom_vec, tfidf_text_counts = build_tfidf_text_counts(features.flora_tokenizer, tokenized_stop_words, flora_data_frame)
tfidf_y_test, tfidf_predictions = run_model(tfidf_text_counts, flora_data_frame, feature_rank=True, custom_vec)
View classified statements¶
In [17]:
dtm_y_test_df = pd.DataFrame(dtm_y_test).reset_index()
dtm_predictions_series = pd.Series(dtm_predictions)
results = pd.concat([dtm_y_test_df, dtm_predictions_series], axis=1)
results.rename(columns={0: 'predictions'}, inplace=True)
results = results.set_index('index')
results_flora_data_frame = pd.concat([results, flora_data_frame], axis=1)
results_flora_data_frame
Out[17]:
In [18]:
incorrect = results[results.classification != results.predictions]
incorrect_data_frame = results_flora_data_frame.iloc[incorrect.index]
incorrect_data_frame.to_csv(path_or_buf = "../reports/incorrect_dtm_clean.csv")
incorrect_data_frame
Out[18]:
Run with strict cleaning regime¶
In [19]:
# ==== DTM =====
custom_vec, dtm_text_counts = build_dtm_text_counts(features.flora_tokenizer_clean, tokenized_stop_words_clean, flora_data_frame)
dtm_y_test, dtm_predictions = run_model(dtm_text_counts, flora_data_frame, feature_rank=True, custom_vec)
# ==== TFIDF =====
custom_vec, tfidf_text_counts = build_tfidf_text_counts(features.flora_tokenizer_clean, tokenized_stop_words_clean, flora_data_frame)
tfidf_y_test, tfidf_predictions = run_model(tfidf_text_counts, flora_data_frame, feature_rank=True, custom_vec)
In [20]:
dtm_y_test_df = pd.DataFrame(dtm_y_test).reset_index()
dtm_predictions_series = pd.Series(dtm_predictions)
results = pd.concat([dtm_y_test_df, dtm_predictions_series], axis=1)
results.rename(columns={0: 'predictions'}, inplace=True)
results = results.set_index('index')
results_flora_data_frame = pd.concat([results, flora_data_frame], axis=1)
results_flora_data_frame
Out[20]:
In [21]:
incorrect = results[results.classification != results.predictions]
incorrect_data_frame = results_flora_data_frame.iloc[incorrect.index]
incorrect_data_frame.to_csv(path_or_buf = "../reports/incorrect_dtm_dirty.csv")
incorrect_data_frame
Out[21]:
Run a model based on text length¶
In [22]:
# Process text, remove stopwords. Remove empty cells.
length_processed_flora_data_frame = features.process_length_in_place(flora_data_frame, tokenized_stop_words)
In [72]:
length_processed_flora_data_frame.to_csv(path_or_buf = "../data/interim/length_processed_flora_data_frame.csv")
In [71]:
classifications = length_processed_flora_data_frame.groupby(by=length_processed_flora_data_frame['classification'])
#bins = np.linspace(-10, 10, 100)
for group in classifications.groups:
# print(group)
group_df = length_processed_flora_data_frame[length_processed_flora_data_frame.classification == group]
group_text_length = group_df['length']
plt.hist(group_text_length, label=group)
#file_name = group + "_text_length.png"
#print(file_name)
#plt.savefig(file_name)
plt.xlim(0, 15000)
plt.ylim(0, 4000)
plt.legend(loc='upper right')
plt.show()
# TO DO
# redo these as overlapping hist with four colours!!!
It looks like discussion should be removed from the dataset. It is curiously short in length. This may be an artifact from the bc dataset.
In [27]:
length_custom_vec = CountVectorizer(lowercase=True, tokenizer=features.flora_tokenizer, stop_words=tokenized_stop_words,
ngram_range=(1, 1))
length_text_counts = length_custom_vec.fit_transform(length_processed_flora_data_frame['text'])
length_model_sparse = features.prepare_length_features(length_text_counts, length_custom_vec, length_processed_flora_data_frame)
X_test, predicted = run_model(length_model_sparse, length_processed_flora_data_frame, feature_rank=False)
To do plots: classification coloured by source
Run a model with only the most frequently occurring words¶
In [28]:
all_text = " ".join(text_string for text_string in flora_data_frame.text)
all_text = features.flora_tokenizer(all_text)
top_words_text = features.find_most_frequent_words(all_text, threshold=2000)
top_words_flora_data_frame = features.filter_data_frame_top_words(flora_data_frame, top_words_text, tokenized_stop_words)
top_words_flora_data_frame
Out[28]:
In [30]:
all_text_custom_vec = CountVectorizer(lowercase=True, tokenizer=features.flora_tokenizer, stop_words=tokenized_stop_words,
ngram_range=(1, 1))
all_text_counts = all_text_custom_vec.fit_transform(top_words_flora_data_frame['text'])
X_test, predicted = run_model(all_text_counts, top_words_flora_data_frame, feature_rank=False)
Do models work well on previously unseen floras?¶
In [42]:
custom_vec, dtm_text_counts = build_dtm_text_counts(features.flora_tokenizer, tokenized_stop_words, flora_data_frame)
In [45]:
dtm_text_counts.toarray()
print(dtm_text_counts.shape)
print(flora_data_frame.shape)
In [59]:
train_indices = flora_data_frame[(flora_data_frame['dataset_name'] =="bc") | (flora_data_frame['dataset_name'] == "fna")].index
X_train = dtm_text_counts[train_indices]
y_train = flora_data_frame.iloc[train_indices].classification
print(X_train.shape)
print(len(y_train))
test_indices = flora_data_frame[flora_data_frame['dataset_name'] =="budds"].index
print(len(test_indices))
X_test = dtm_text_counts[test_indices]
y_test = flora_data_frame.iloc[test_indices].classification
In [60]:
clf = MultinomialNB().fit(X_train, y_train)
predicted = clf.predict(X_test)
print("MultinomialNB Accuracy:", metrics.accuracy_score(y_test, predicted))
print(classification_report(y_test, predicted))
class_labels = clf.classes_
print_top10(custom_vec, clf, class_labels)
In [63]:
dtm_y_test_df = pd.DataFrame(y_test).reset_index()
dtm_predictions_series = pd.Series(predicted)
results = pd.concat([dtm_y_test_df, dtm_predictions_series], axis=1)
results.rename(columns={0: 'predictions'}, inplace=True)
results = results.set_index('index')
results_flora_data_frame = pd.concat([results, flora_data_frame], axis=1, join='inner')
results_flora_data_frame
Out[63]:
Running a baseline model!¶
In [ ]:
baseprediction = zero_rule_algorithm_classification(line_features, labels) # get predictions for baseline
if baseprediction[0] == 0:
baseline = (len(baseprediction) - np.count_nonzero(labels)) / (len(baseprediction))
else:
baseline = (len(baseprediction) - len(np.where(labels == 0))) / (len(baseprediction))
print(f"Baseline score: {baseline}")